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Also, identified a bug where the\nstrand would be set to unknown if an independent strand was provided.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/9ff0387a95fb0437860219754c1bb51cf8328258"},{"sha":"2eec1afadc988238cb426361c017f2a5ef5a97a4","author":{"name":"Justin Paschall","email":"8dbdfd508419566e1b0533b5c76990630a0621a0@gmail.com"},"message":"Added docs about running on Slurm","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/2eec1afadc988238cb426361c017f2a5ef5a97a4"},{"sha":"12aaa7b385645631fe8ee786b75af5743921f085","author":{"name":"Justin Paschall","email":"8dbdfd508419566e1b0533b5c76990630a0621a0@gmail.com"},"message":"fix slurm docs typos","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/12aaa7b385645631fe8ee786b75af5743921f085"},{"sha":"c157ab8c7b6de797e400a239e9909612fbe10129","author":{"name":"Paschall","email":"59d1b5fff880f5b756000a9d0b2cc402c212a0b0@HG-01931188-LM1.local"},"message":"Moved Slurm docs to existing 40_deploying_ADAM.md and addressed comments","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/c157ab8c7b6de797e400a239e9909612fbe10129"},{"sha":"8572fb7e8f32c78580306c9a685d07b9cca5e54e","author":{"name":"Justin Paschall","email":"8dbdfd508419566e1b0533b5c76990630a0621a0@gmail.com"},"message":"addressed  review comments","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/8572fb7e8f32c78580306c9a685d07b9cca5e54e"},{"sha":"0e92cfe1fc9f2fa5d7e0cf65a56c42f45ec0c316","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1417] Removed unused Projection.apply method, add test for Filter.\n\nResolves #1417.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/0e92cfe1fc9f2fa5d7e0cf65a56c42f45ec0c316"},{"sha":"9eaefdc604756a0ecf9733f0af3d3cf467f9ff37","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1047] Support generating predicates from `ReferenceRegion`s.\n\nResolves #1047.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/9eaefdc604756a0ecf9733f0af3d3cf467f9ff37"},{"sha":"acb0c0731da1644c8222fa5af4926d54e93a9885","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1539] Support region predicate in TransformAlignments.\n\nResolves #1539.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/acb0c0731da1644c8222fa5af4926d54e93a9885"},{"sha":"e55a6ab099e03591b8f61fa386f9d51619c5a4ab","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Revert slf4j dependency changes from 9505d47e881305367fbad4bdfb8f189c3e766b0a.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/e55a6ab099e03591b8f61fa386f9d51619c5a4ab"},{"sha":"253a1becac513fef84baccd48cfef352aabf6c19","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"Flesh out Java APIs in GenomicRDDs.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/253a1becac513fef84baccd48cfef352aabf6c19"},{"sha":"c34a44004f80d4958df40eed6ae5d3760b8317ae","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-538] Add support for an adam-python API.\n\nResolves #538. Adds support for Python APIs that use the ADAM Java API to make\nthe ADAMContext and RDD functions accessible natively through python.","distinct":false,"url":"https://api.github.com/repos/fnothaft/adam/commits/c34a44004f80d4958df40eed6ae5d3760b8317ae"},{"sha":"a59b8ed948db1bbf50260a61ed404b8325df0563","author":{"name":"Frank Austin Nothaft","email":"d9347962c16e697d97aca23107f7a15117076855@alumni.stanford.edu"},"message":"[ADAM-1018] Add support for Spark SQL Datasets.\n\nResolves #1018. Adds the `adam-codegen` module, which generates classes that:\n\n1. Implement the Scala Product interface and thus can be read into a Spark SQL\nDataset.\n2. Have a complete constructor that is compatible with the constructor that\nSpark SQL expects to see when exporting a Dataset back to Scala.\n3. And, that have methods for converting to/from the bdg-formats Avro models.\n\nThen, we build these model classes in the `org.bdgenomics.adam.sql` package,\nand use them for export from the Avro based GenomicRDDs. With a Dataset, we\ncan then export to a DataFrame, which enables us to expose data through\nPython via RDD->Dataset->DataFrame. 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